hi everyone. i am a beginner PhD student in the field of md simulation and want to use umbrella sampling to study the permeation of my nanoparticle through a membrane. my system contains “ions, water, nanoparticle and membrane”
i prepared 2 groups in my index file: (1) nano | (2) other (contain membrane, water and ion). is it correct as i just want to pull my nanoparticle?
so is this pulling code in my mdp file ok or i should modify it?
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = other
pull_group2_name = nano
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = direction ; simple distance increase
pull_coord1_vec = 0 0 1
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
If you want to pull a nanoparticle through a membrane, you should not pull on everything else.
You should use:
pull_group1_name = membrane
pull_group2_name = nano
pull_coord1_geometry = cylinder
But a nanoparticle sounds too large to get good sampling for. In addition your setup currently does steered MD, not umbrella sampling. It might be good to look at a tutorial first.
dear hess,
thank you for your reply.
you are right i first wanted to do SMD, and then umbrella sampling.
i am simulating my self-assembled nanoparticles first which have about 3nm diameter. my membrane has 4 nm thickness. do you think that this condition may not a have good sampling result? so what should i do?
i modified my code in such way: is it good?
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = membrane
pull_group2_name = nano
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ;
pull_coord1_start = yes ; define initial COM distance > 0
pull-pbc-ref-prev-step-com = yes
pull-coord1-geometry = cylinder
pull_coord1_vec = 0.0 0.0 1.0
pull_coord1_rate = 0.0001 ;
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Dear hess.
thank you so much.
i have now another question, besides umbrella sampling, which kind of other sampling ways may be a good choice for my system?
is Adaptive weighted histogram (AWH) method a good one in this case?
The goal here is to just compare the interaction and permeation of different nanoparticles through a model cell membrane to identify which one is more favorable than another.
If yes, is there a tutorial like this tutorial for umbrella sampling that describes the exact steps of how to do this method and how to prepare the relevant files and commands (not necessarily basic and general concepts)? (Umbrella Sampling)
And whether the results of this method will be comparable to umbrella sampling in the end?
Dear hess.
thank you so much.
i have now another question, besides umbrella sampling, which kind of other sampling ways may be a good choice for my system?
is Adaptive weighted histogram (AWH) method a good one in this case?
The goal here is to just compare the interaction and permeation of different nanoparticles through a model cell membrane to identify which one is more favorable than another.
If yes, is there a tutorial like this tutorial for umbrella sampling that describes the exact steps of how to do this method and how to prepare the relevant files and commands (not necessarily basic and general concepts)? (Umbrella Sampling)
And whether the results of this method will be comparable to umbrella sampling in the end?